deal with nexson otus that don't have ottol ids before adding to graph

[blackrim]

deal with nexson otus that don't have ottol ids before adding to graph

[jar398]

On Wed, Mar 27, 2013 at 9:03 AM, Stephen Smith [email protected]:

we need to be able to deal with these before they are added to the graph.
The idea would be to

1. TNRS the names that are there

• For ones that match that weren't matched before, we can assign the
  ottol id
  1. For remaining names, if there are any, retrieve the scope
     determined by the TNRS
     • Add these remaining names as names subtending the scope name to the
       taxonomy WITHIN treemachine
• Add these new names to an index that identifies these as new names
  and give a temp ottol id. This index will serve as easy way to update once
  we have new official ids from taxomachine and will serve to easily update
  taxomachine

Be sure this index links back to the study (i.e. contains the study id)!
The study is the only "authority" for the name that we'd have at this
point.

Jonathan

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[blackrim]

Will do and this is related to OpenTreeOfLife/taxomachine#16

[blackrim]

Cant seem to get the TNRS to connect with URLConnection or HttpUrlConnection. Not sure the problem but if someone wants to take a look it is on lines 105-150 in PhylografterConnector. Keep getting 406 with just the simplest call (not post, just the basic call that is the curl http://opentree-dev.bio.ku.edu:7476/db/data/ext/TNRS/graphdb/getContextForNames

[chinchliff]

There is an example of doing a http post request using the jersey library in taxomachine in opentree.tnrs/TNRSAdapterGNR.java. It was working for me before, although who knows, I don't think the GNR uses neo4j. Anyway the maven dependency is the com.sun.jersey.jersey-client, it's also in the taxomachine pom.xml (and the pom.serverplugins.xml)

[chinchliff]

So, I switched the PhylografterConnector code over to using the jersey client objects. It now connects successfully to the TNRS context query. Presumably it should be easy to recycle the code for the name queries. Not sure what the next step is in the workflow though (getting the names phylografter doesn't know?) so I have just left it alone for now. Let me know if there is other stuff for me to help with.

[blackrim]

Excellent. Thanks cody. I can deal with the next steps when I get back

On Mon, Apr 1, 2013 at 10:19 AM, chinchliff [email protected]:

So, I switched the PhylografterConnector code over to using the jersey
client objects. It now connects successfully to the TNRS context query.
Presumably it should be easy to recycle the code for the name queries. Not
sure what the next step is in the workflow though (getting the names
phylografter doesn't know?) so I have just left it alone for now. Let me
know if there is other stuff for me to help with.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/21#issuecomment-15725288
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[blackrim]

the TNRS part is basically done now with the help of cody and joseph. i just got the final step in there and am working on putting the taxa that don't match (which aren't that many so far)

[blackrim]

everything is done for the adding nodes except the actual adding. working out the temp ids and then it should be done